Mercker was taken in the first round (5th pick overall) of the amateur draft by the Atlanta Braves. He made his Major League debut with the Braves on September 22, and appeared in two games that season.
During his years with the Braves, Mercker split time between the bullpen and the starting rotation. After serving as a reliever for the vast part of his first five seasons, he joined the Braves' rotation full time for the and seasons.
After the 1995 season, the Braves traded Mercker to the Baltimore Orioles. Mercker has been a journeyman ever since, spending time with Baltimore Cleveland (1996), Cincinnati (, -), St. Louis (-), Boston (1999), Anaheim Colorado Atlanta (2003), and the Chicago Cubs (). During the 2004 season, Mercker reportedly called the broadcast booth to complain about commentary by Steve Stone and, along with Moisés Alou, confronted Stone on a team flight. He signed with Cincinnati for the third time in his career on December 20, 2004.
Mercker has taken part in two no-hit games during his career, both with the Braves. The first, on September 11, against the San Diego Padres at Fulton County Stadium, was a combined effort between Mercker, the starter, who pitched six innings; Mark Wohlers, who pitched the seventh and eighth innings; and Alejandro Pena, who pitched the ninth. The Braves defeated the Padres 1-0. The second no-hitter was a solo effort by Mercker, as he no-hit the Los Angeles Dodgers on April 8, 1994 at Dodger Stadium in a 6-0 victory. To date, this no-hitter is the last to be pitched by a Brave.